Tree of Life

Version 2.0 is available!

Don't miss out on the new among-site-rate-variation-aware iterative Neighbor Joining (see the user manual for more information)

SEMPHY - version 2.0-b3 - April, 2008

Download code, user manual and executables:

source code of SEMPHY 2.0b3 (md5sum is "b13a14c16d42ebfef31770654b23bc4b semphy-2.0b3.tgz")
User manual for version 2.0b3
precompiled for Linux kernel 2.6 on i386
precompiled for Macintosh: macintel and PowerPc
precompiled for Windows: semphy.exe and in "doubleRep" form ready for big (>300 taxa) trees semphy.doubleRep.exe. See the user manual for more information

Installation

(from source code. if you download an executable - simply run it!)
Unpack:
> tar xzvf semphy-2.0b2.tgz
Go into the top directory:
> cd semphy
Compile
> make all
Test: (there may be some minor diffs between the outputs of the tests and the target outputs that come from precision or order of leaves on trees, so if you do get some minor differences of this sort, your installation is probably still OK)
> make test
And install the executables into the bin directory
> make install
This will place all semphy executables in the "semphy/bin" directory.

SEMPHY - version 1.0-a5 - February, 2004

Summary

SEMPHY is a tool for maximum likelihood phylogenetic reconstruction. It uses Structural EM, to search for the maximum likelihood tree topology efficiently and effectively in large datasets.

The version available here our development version. We have a stable version available as well. This version supports rate variation, the WAG and cpREV replacement matrices, as well as user matrices. Several bugs that affected stability have been eliminated in this version, and all our current tests seem to work fine.

Main Features:
  • Up to about 100 taxa
  • supports rate-variation with the Gamma model, including alpha optimization
  • Supports several Amino acid models
  • supports user inputed Amino acid repayment models
  • Supports most of the standard file types

    supported platforms:
  • Linux (with gcc/g++3)
  • Apple - Mac OSX (with gcc/g++3)
  • Windows 95/98/NT and probably 2000 and XP using VC (may need "getopts"), or cygwin
  • FreeBSD


    • Compatibility with additional platforms :
  • Solaris (needs "getopts")
  • irix (needs "getopts")
  • Windows XP using cygwin

    On platforms that do not have GNU style "getopts", you will need to comment out line 30 of the Makefile in the lib directory, which deals with the "getopt" code.

    Warning: this code will not work with g++-2.96, as the resulting executable will perform unpredictably. gcc/g++ 3.3 was tested, and works, g++-2.95 may work. gcc/g++ can be downloaded here.

    Please inform us if you succeed to compile and run this on any platform other then Linux, together with the type of compiler used, so we could update this page and help others with the compilations. If you encounter compilation problems you can contact us, and we will try to help you. We can be reached at semphy@cs.huji.ac.il.

     

    compilation:
    > cd lib
    > make all
    > cd ..
    > make all

    You can test if the compiled code came out ok by running
    > make -k test
    after each "make all" above - this will run a set of tests and check that the output is exactly as expected.
    (please note that this step may fail if "tcsh" is not present or not where the scripts expect to find it. - such a problem will not influence SEMPHY itself.)

    Historical versions

    Executables

    SEMPHY 2.0b2

    precompiled for Linux kernel 2.6 on i386
    precompiled for Macintosh: macintel and PowerPc
    precompiled for Windows: semphy.exe and in "doubleRep" form ready for big (>300 taxa) trees semphy.doubleRep.exe. See

    SEMPHY 1.0

    SEMPHY 1.0a5 OS-X precompiled (md5sum is "2a07a96894ebaf913c9da36d723464e6 semphy-1.0a5-osx.gz")
    (compiled with g++ 3.3, on Darwin, with Kernel Version 7.3.0
    SEMPHY 1.0a5 Linux precompiled (md5sum is "fadceb2ebeb8ffa64a36f213069a1304 semphy-1.0a5.gz")
    (compiled with g++ 3.3.2, on linux with a 2.4.35 kernel

    Code

    SEMPHY 2.0b2 (md5sum is "eec9f6d2ea28e0cfa2f8c89fb7d021ae semphy-2.0b2.tgz")
    SEMPHY 1.0a5 (md5sum is "ddee74d840136093bb37aa18a4e2b912 semphy-1.0a5.tgz")
    SEMPHY 1.0a4 (md5sum is "e2f6c31c62e2186d035f52c9b8eefe83 semphy-1.0a4.tgz")
    SEMPHY 1.0a3 (md5sum is "c194190207c025533d4405d2358f2ec2 semphy-1.0a3.tgz")
    SEMPHY 1.0a2 (md5sum is "dd6a9ab9215c2fb9a992922afa0fa991 semphy-1.0a2.tgz")
    SEMPHY 1.0a1 (md5sum is "83fbdc19e7476d95ed481fb0e8803cbb semphy-1.0a1.tgz")
    getopts